<tool id="make_decoy" name="Generate protein decoy sequences" version="1.0.1">
    <description>
        Generate random protein sequences with the same AA composition as input sequences
    </description>
    <requirements>
        <container type="docker">iracooke/protk-1.4.3</container>
        <requirement type="package" version="1.4.3">protk</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Failure" />
    </stdio>
    <command>
        make_decoy.rb $fasta_file -o $output -P $prefix_string $append
    </command>
    <inputs>
        <param name="fasta_file" type="data" format="fasta" label="Fasta file contain protein sequences" />
        <param name="prefix_string" help="Prefix String to use for Decoys" type="text" value="decoy_" label="Prefix String" size="20"/>        
        <param name="append" type="boolean" label="Append input sequences to the generated sequences" help="" truevalue="--append" falsevalue="" />
    </inputs>
    <outputs>
        <data format="fasta" name="output" />
    </outputs>
    <tests>
      <test>
          <param name="fasta_file" value="testdb.fasta" format="fasta"/>
          <output name="output" format="fasta">
              <assert_contents>
                  <has_text text="decoy_rp3" />
              </assert_contents>
          </output>
      </test>
    </tests>
    <help>

**What it does**

Generates random protein sequences based on the amino acid composition of a given set of input sequences. To be used for decoy proteomics searches


    </help>
</tool>